Browse
Submit Data
Databases
API
Help

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification and Whole-Genome Sequencing of a Monkeypox Virus Strain Isolated in Israel.

ABSTRACT: We report the whole-genome sequence of a monkeypox virus strain isolated in Israel. The strain was isolated in 2018 from a patient travelling back from West Africa. The virus was fully sequenced on the Illumina MiSeq and Oxford Nanopore Technologies MinION platforms.

SUBMITTER: Cohen-Gihon I

PROVIDER: S-EPMC7171222 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Identification and Whole-Genome Sequencing of a Monkeypox Virus Strain Isolated in Israel.

Cohen-Gihon Inbar I Israeli Ofir O Shifman Ohad O Erez Noam N Melamed Sharon S Paran Nir N Beth-Din Adi A Zvi Anat A

Microbiology resource announcements 20200305 10

We report the whole-genome sequence of a monkeypox virus strain isolated in Israel. The strain was isolated in 2018 from a patient travelling back from West Africa. The virus was fully sequenced on the Illumina MiSeq and Oxford Nanopore Technologies MinION platforms. ...[more]

PMID: 32139560

Similar Datasets

Whole-Genome Sequence of a Human Monkeypox Virus Strain Detected in Egypt.

Project description:Monkeypox virus has recently been detected in multiple countries. Two cases of monkeypox virus were reported in Egypt as part of an ongoing international outbreak. We report the whole-genome sequence of a monkeypox virus that was retrieved from the first confirmed case in Egypt. The virus was fully sequenced on the Illumina platform, and phylogenetic analysis demonstrated that the current monkeypox strain is closely related to clade IIb, which caused recent multicountry outbreaks.

| S-EPMC10281154 | biostudies-literature

Complete Genome Sequences of Monkeypox Virus from a French Clinical Sample and the Corresponding Isolated Strain, Obtained Using Nanopore Sequencing.

Project description:We report the whole-genome sequences of a monkeypox virus from the skin lesion of a French patient and the corresponding isolated viral strain. Both viral genomic sequences were successfully obtained by applying shotgun metagenomics using the Oxford Nanopore Technologies sequencing approach.

| S-EPMC10112124 | biostudies-literature

Targeted amplification-based whole genome sequencing of <i>Monkeypox virus</i> in clinical specimens.

Project description:ImportanceWe present a protocol to efficiently sequence genomes of the MPXV-causing mpox. This enables researchers and public health agencies to acquire high-quality genomic data using a rapid and cost-effective approach. Genomic data can be used to conduct surveillance and investigate mpox outbreaks. We present 91 mpox genomes that show the diversity of the 2022 mpox outbreak in Ontario, Canada.

| S-EPMC10783113 | biostudies-literature

Whole genome sequencing and taxonomic profiling of two Pantoea sp. isolated from environmental samples in Israel.

Project description:ObjectiveAs part of a research aiming at the isolation of bacteria secreting growth inhibiting compounds, cultures of Francisella tularensis were implanted in environmental samples and monitored for inhibition zones on agar. Two antibiotic-like secreting bacteria were isolated, their genomic sequence was deciphered and taxonomic profiling analysis classified them as belonging to the Pantoea genus.Data descriptionTwo bacterial isolates exhibiting growth inhibition zones to F. tularensis (LVS) were analyzed using the Oxford Nanopore Technology (ONT). Preliminary de novo assembly of the reads was performed, followed by taxonomic profiling based on Multi Locus Sequence Analysis (MLSA) and implementation of the Average Nucleotide Identity (ANI) measure. The genomic sequences resulted in the identification of two different Pantoea species, denoted EnvD and EnvH. Subsequent de novo genome assembly generated 5 and 10 contigs for EnvD and EnvH, respectively. The largest contig (4,008,183 bps and 3,740,753 bps for EnvD and EnvH, respectively), overlaps to a major extent to the chromosome of closely related Pantoea species. ANI values calculated for both isolates revealed two apparently new species of the Pantoea genus. Our study deciphered the identity of two bacteria producing antibiotic-like compounds, and the genomic sequence revealed they represent distinct Pantoea species.

| S-EPMC9022320 | biostudies-literature

Whole-Genome Sequencing of Clostridium sp. Strain FP2, Isolated from Spoiled Venison.

Project description:Clostridium sp. strain FP2 was isolated from vacuum-packaged refrigerated spoiled venison in New Zealand. This report describes the generation and annotation of the 5.6-Mb draft genome sequence of Clostridium sp. FP2, which will facilitate future functional genomic studies to improve our understanding of premature spoilage of red meats.

| S-EPMC7193938 | biostudies-literature

Whole-Genome Sequencing of Pasteurella multocida Strain Pm1, Isolated from a Calf.

Project description:Bovine pneumonia is a disease that causes significant economic losses in livestock industries and is vital for animal welfare. The whole-genome sequence of Pasteurella multocida strain Pm1, isolated from a calf suffering from pneumonia in Japan, is reported here.

| S-EPMC9022573 | biostudies-literature

Nanopore sequencing of a monkeypox virus strain isolated from a pustular lesion in the Central African Republic.

Project description:Monkeypox is an emerging and neglected zoonotic disease whose number of reported cases has been gradually increasing in Central Africa since 1980. This disease is caused by the monkeypox virus (MPXV), which belongs to the genus Orthopoxvirus in the family Poxviridae. Obtaining molecular data is particularly useful for establishing the relationships between the viral strains involved in outbreaks in countries affected by this disease. In this study, we evaluated the use of the MinION real-time sequencer as well as different polishing tools on MinION-sequenced genome for sequencing the MPXV genome originating from a pustular lesion in the context of an epidemic in a remote area of the Central African Republic. The reads corresponding to the MPXV genome were identified using two taxonomic classifiers, Kraken2 and Kaiju. Assembly of these reads led to a complete sequence of 196,956 bases, which is 6322 bases longer than the sequence previously obtained with Illumina sequencing from the same sample. The comparison of the two sequences showed mainly indels at the homopolymeric regions. However, the combined use of Canu with specific polishing tools such as Medaka and Homopolish was the best combination that reduced their numbers without adding mismatches. Although MinION sequencing is known to introduce a number of characteristic errors compared to Illumina sequencing, the new polishing tools allow a better-quality MinION-sequenced genome, thus to be used to help determine strain origin through phylogenetic analysis.

| S-EPMC9232561 | biostudies-literature

Complete Genome Sequence of Monkeypox Virus Strain MPXV-ROK-P1-2022 Isolated from the First Monkeypox Patient in the Republic of Korea.

Project description:We report the complete genome sequence of the monkeypox virus strain MPXV-ROK-P1-2022, isolated from the first patient diagnosed with monkeypox in the Republic of Korea in June 2022. The virus was fully sequenced on the Illumina MiSeq instrument, and the phylogenetic tree showed that the strain belongs to lineage B.1.1.

| S-EPMC9670986 | biostudies-literature

Whole-Genome Sequencing of Macrolide-Resistant Mycoplasma pneumoniae Strain S355, Isolated in China.

Project description:Macrolide-resistant Mycoplasma pneumoniae plays an important role in refractory M. pneumoniae pneumonia. Here, we present the whole-genome sequencing of the macrolide-resistant M. pneumoniae strain S355. The annotated full-genome sequence might provide a new insight into drug resistance in M. pneumoniae and can help pediatricians recognize the disease earlier.

| S-EPMC4796115 | biostudies-literature

Whole-Genome Sequencing of a Mycobacterium orygis Strain Isolated from Cattle in Chennai, India.

Project description:Here, we report the isolation of Mycobacterium orygis from dairy cattle in Chennai, India. Spoligotyping assigned the isolate to spoligotype 587 (ST587), which belongs to M. orygis This species was confirmed as M. orygis using whole-genome sequencing.

| S-EPMC6776786 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data